library(seqinr)
library(multicore)
library(BioPhysConnectoR)
Spec_iGEM_Clustalo.R<-function(){}

clustalo <- function(x,cores, exec = NULL,quiet = TRUE,mod=T)
  os <- Sys.info()[1] 
  exec <- "clustalo"  
	Name<-basename(x) 
	Name.oext<-sub("^([^.]*).*", "\\1", Name)
	Name.out<-paste0(Name.oext,"_aln.fa",sep="",collapse=NULL)
	Name.ph<-paste0(Name.oext,"_aln.ph",sep="",collapse=NULL)

  i.file<-paste0("-infile=",Name,sep="",collapse=NULL)
  o.file<-paste0("-outfile=",Name.out,sep="",collapse=NULL)	
  o.tree<-paste0("--guidetree-out=",Name.ph,sep="",collapse=NULL)	
  opt.in<-paste0("--dealign ","--threads=",cores," --outfmt=fasta",collapse=NULL,sep="")	
	input<-paste(i.file,o.file,o.tree,opt.in)
  command<-paste(exec,input)	
  system(command,wait=T,intern=F)
 
	return(BioPhysConnectoR::read.fasta(paste(getwd(),Name.out,sep="/",collapse=NULL)))	

}
